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Table 3 The breakdown of the running time (in CPU hours) for HAPiID

From: Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data

  HM403 HM415 HM454 HM455 HM466 HM467 HM494 HM503
HAPiID DB (targeted search) 76,663 67,537 79,813 84,304 89,693 73,905 94,395 73,766
HAPiID time (profiling) 4.02 4.05 3.23 3.843 3.47 3.36 3.95 3.92
HAPiID time (targeted search) 4.46 4.57 4.49 5.63 5.64 4.33 6.35 5.13
HAPiID time (total) 8.48 8.62 7.72 9.473 9.11 7.69 10.3 9.05
MS-GF+ time (IGC db search) 367.95 485.79 413.58 510.47 462.47 405.86 503.33 495.22
  1. *The row shows the sizes of the target databases (for the second targeted search step) in HAPiID, which contains putative proteins from top n most abundant genomes covering 80% of the total spectra during profiling step. These numbers vary slightly across samples. For comparison, the target databases for the HAPiID’s first search step (i.e., HAPdb) and the MetaPro-IQ’s first step (i.e., IGC db) contain 1.1×105 and 9.8×106 proteins, respectively.
  2. **For comparison purpose, we ran MS-GF+ search against the massive target database (IGC db) used in the MetaPro-IQ’s first step to estimate the lower bound of the running time for the MetaPro-IQ pipeline.